[2024-01-24 10:47:24,608] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:24,615] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:24,616] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b335a7b-75bb-49c3-9114-ef51ebe03e54/dqc_reference
[2024-01-24 10:47:26,557] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:26,558] [INFO] Task started: Prodigal
[2024-01-24 10:47:26,559] [INFO] Running command: gunzip -c /var/lib/cwl/stg23942195-4431-4969-a7b6-37473bbaee05/GCF_019048805.1_ASM1904880v1_genomic.fna.gz | prodigal -d GCF_019048805.1_ASM1904880v1_genomic.fna/cds.fna -a GCF_019048805.1_ASM1904880v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:41,433] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:41,433] [INFO] Task started: HMMsearch
[2024-01-24 10:47:41,434] [INFO] Running command: hmmsearch --tblout GCF_019048805.1_ASM1904880v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b335a7b-75bb-49c3-9114-ef51ebe03e54/dqc_reference/reference_markers.hmm GCF_019048805.1_ASM1904880v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:41,747] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:41,749] [INFO] Found 6/6 markers.
[2024-01-24 10:47:41,797] [INFO] Query marker FASTA was written to GCF_019048805.1_ASM1904880v1_genomic.fna/markers.fasta
[2024-01-24 10:47:41,797] [INFO] Task started: Blastn
[2024-01-24 10:47:41,797] [INFO] Running command: blastn -query GCF_019048805.1_ASM1904880v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b335a7b-75bb-49c3-9114-ef51ebe03e54/dqc_reference/reference_markers.fasta -out GCF_019048805.1_ASM1904880v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:42,642] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:42,645] [INFO] Selected 18 target genomes.
[2024-01-24 10:47:42,646] [INFO] Target genome list was writen to GCF_019048805.1_ASM1904880v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:42,653] [INFO] Task started: fastANI
[2024-01-24 10:47:42,653] [INFO] Running command: fastANI --query /var/lib/cwl/stg23942195-4431-4969-a7b6-37473bbaee05/GCF_019048805.1_ASM1904880v1_genomic.fna.gz --refList GCF_019048805.1_ASM1904880v1_genomic.fna/target_genomes.txt --output GCF_019048805.1_ASM1904880v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:01,802] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:01,803] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b335a7b-75bb-49c3-9114-ef51ebe03e54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:01,803] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b335a7b-75bb-49c3-9114-ef51ebe03e54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:01,820] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:48:01,820] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:01,820] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Citrobacter braakii	strain=FDAARGOS 1421	GCA_019048805.1	57706	57706	type	True	100.0	1859	1859	95	conclusive
Citrobacter braakii	strain=ATCC 51113	GCA_002075345.1	57706	57706	type	True	99.965	1791	1859	95	conclusive
Citrobacter europaeus	strain=97/79	GCA_900079995.3	1914243	1914243	type	True	93.3243	1392	1859	95	below_threshold
Citrobacter arsenatis	strain=LY-1	GCA_004353845.1	2546350	2546350	type	True	93.0619	1423	1859	95	below_threshold
Citrobacter portucalensis	strain=A60	GCA_002042885.1	1639133	1639133	type	True	92.5105	1346	1859	95	below_threshold
Citrobacter freundii	strain=ATCC 8090	GCA_011064845.1	546	546	type	True	92.4207	1381	1859	95	below_threshold
Citrobacter freundii	strain=NBRC 12681	GCA_000759735.1	546	546	type	True	92.3656	1345	1859	95	below_threshold
Citrobacter pasteurii	strain=FDAARGOS 1424	GCA_019047765.1	1563222	1563222	type	True	90.0512	1301	1859	95	below_threshold
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	83.0682	1003	1859	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	83.0138	1061	1859	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.6899	868	1859	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	81.6256	890	1859	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.3624	872	1859	95	below_threshold
Aeromonas jandaei	strain=FDAARGOS_1523	GCA_020341535.1	650	650	type	True	78.0942	117	1859	95	below_threshold
Aeromonas jandaei	strain=FDAARGOS_986	GCA_016127195.1	650	650	type	True	78.0204	115	1859	95	below_threshold
Aeromonas allosaccharophila	strain=CECT 4199	GCA_000819685.1	656	656	type	True	76.9283	111	1859	95	below_threshold
Aeromonas jandaei	strain=CECT 4228	GCA_000819955.1	650	650	type	True	76.7288	100	1859	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:01,822] [INFO] DFAST Taxonomy check result was written to GCF_019048805.1_ASM1904880v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:01,822] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:01,823] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:01,823] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b335a7b-75bb-49c3-9114-ef51ebe03e54/dqc_reference/checkm_data
[2024-01-24 10:48:01,824] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:01,874] [INFO] Task started: CheckM
[2024-01-24 10:48:01,874] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019048805.1_ASM1904880v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019048805.1_ASM1904880v1_genomic.fna/checkm_input GCF_019048805.1_ASM1904880v1_genomic.fna/checkm_result
[2024-01-24 10:48:48,372] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:48,373] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:48,410] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:48,410] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:48,411] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019048805.1_ASM1904880v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:48,411] [INFO] Task started: Blastn
[2024-01-24 10:48:48,412] [INFO] Running command: blastn -query GCF_019048805.1_ASM1904880v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b335a7b-75bb-49c3-9114-ef51ebe03e54/dqc_reference/reference_markers_gtdb.fasta -out GCF_019048805.1_ASM1904880v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:49,616] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:49,622] [INFO] Selected 11 target genomes.
[2024-01-24 10:48:49,622] [INFO] Target genome list was writen to GCF_019048805.1_ASM1904880v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:49,631] [INFO] Task started: fastANI
[2024-01-24 10:48:49,632] [INFO] Running command: fastANI --query /var/lib/cwl/stg23942195-4431-4969-a7b6-37473bbaee05/GCF_019048805.1_ASM1904880v1_genomic.fna.gz --refList GCF_019048805.1_ASM1904880v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019048805.1_ASM1904880v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:03,371] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:03,390] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:03,390] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_002075345.1	s__Citrobacter braakii	99.965	1791	1859	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.63	96.30	0.86	0.77	154	conclusive
GCF_900079995.3	s__Citrobacter europaeus	93.3279	1391	1859	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.13	99.04	0.92	0.90	21	-
GCF_004353845.1	s__Citrobacter freundii_E	93.0619	1423	1859	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.27	99.27	0.92	0.92	2	-
GCF_002042885.1	s__Citrobacter portucalensis	92.5105	1346	1859	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.01	95.95	0.89	0.83	128	-
GCF_011064845.1	s__Citrobacter freundii	92.4242	1380	1859	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.70	97.40	0.89	0.80	446	-
GCF_018035235.1	s__Citrobacter freundii_A	92.0755	1355	1859	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.33	99.24	0.91	0.90	6	-
GCF_000155975.1	s__Citrobacter portucalensis_A	91.1428	1330	1859	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900759445.1	s__Klebsiella sp900759445	91.0941	744	1859	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003818115.1	s__Citrobacter youngae	90.1935	1287	1859	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	97.80	95.31	0.91	0.87	45	-
GCF_000819955.1	s__Aeromonas jandaei	76.6679	101	1859	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.8323	96.79	96.38	0.92	0.87	26	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:03,392] [INFO] GTDB search result was written to GCF_019048805.1_ASM1904880v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:03,393] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:03,397] [INFO] DFAST_QC result json was written to GCF_019048805.1_ASM1904880v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:03,397] [INFO] DFAST_QC completed!
[2024-01-24 10:49:03,397] [INFO] Total running time: 0h1m39s